Raw mass spectrometry data were analyzed by MS-DIAL software using standard protocols. MS peaks with MS/MS spectra were collected and identified using publicly available databases and in-house database by comparing the similarity of MS spectra and MS/MS profile, followed by verifying retention times. Some of identified metabolites were confirmed with chemical standards. The metabolic profile differences across groups were assessed using PCA with a permutational multivariate analysis of variance (PERMANOVA) statistical test. Student's t-test with P < 0.05 and partial least squares-discriminant analysis (PLS-DA) with a VIP value > 1 were used to screen differential metabolites between two groups, while ANOVA with Tukey’s test P < 0.05 was used to screen differential metabolites among multiple groups. Additional information regarding metabolomic analysis is available elsewhere.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - reverse-phase"],"chromatography_protocol":["Root samples (0.50 g) were homogenized in a methanol solution (80% v/v, 4 mL). Following a 15-minute vortexing, the mixture was centrifuged at 12,000 × g for 10 minutes. The supernatant was then filtered through a 0.22 μm filter into brown autosampler vials for metabolomic analysis.
Metabolic profile for each sample was detected using a Sciex TripleTOF 5600+ coupled with a Shimadzu LC-20A HPLC. Electrospray ionization (ESI) in both positive and negative modes was performed for mass spectrometry. The chromatographic column was a Waters XSelect HSS T3 column (4.6×150 mm, 3.5 µm) with the flow rate set at 0.30 mL/min. Mobile phase A was prepared using 0.1% formic acid solution for positive ionization mode and 5 mM ammonium formate solution for negative ionization mode. Mobile phase B consisted of acetonitrile and was programmed at 1% for 0−3.0 min, from 1% to 100% with a linear ramp for 3.1−24.0 min, 100% for 24.1−32.0 min, and 1% for 32.1−37.0 min.
"],"publication":["Plants establish metabolic crosstalk with Pseudomonas for enhancing herbicide-stress resistance."],"submitter_affiliation":["Zhejiang University of Technology"],"submitter_name":["B S"],"organism_part":["root tissues"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["B. rapa seedlings were cultivated in a nutrient solution containing 0.2 mg/L Nico alone, a combination of 0.2 mg/L Nico and 0.1 mg/L DBA, 0.1 mg/L DBA alone, and an untreated control group. After 24 hours of cultivation, root tissues were collected for the assessment of physiological indices, transcriptomic profiling, and metabolomic analysis.
"],"organism":["Brassica rapa var. perviridis"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15629"],"author":["Yong Li. Institute of Food Safety and Nutrition, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, 210014, China. liyong201508@jaas.ac.cn."],"data_transformation_protocol":["Raw mass spectrometry data were analyzed by MS-DIAL software using standard protocols. MS peaks with MS/MS spectra were collected and identified using publicly available databases and in-house database by comparing the similarity of MS spectra and MS/MS profile, followed by verifying retention times. Some of identified metabolites were confirmed with chemical standards. The metabolic profile differences across groups were assessed using PCA with a permutational multivariate analysis of variance (PERMANOVA) statistical test. Student's t-test with P < 0.05 and partial least squares-discriminant analysis (PLS-DA) with a VIP value > 1 were used to screen differential metabolites between two groups, while ANOVA with Tukey’s test P < 0.05 was used to screen differential metabolites among multiple groups. Additional information regarding metabolomic analysis is available elsewhere.
"],"study_factor":["Treatment"],"submitter_email":["253313593@qq.com"],"sample_collection_protocol":["B. rapa seedlings were cultivated in a nutrient solution containing 0.2 mg/L Nico alone, a combination of 0.2 mg/L Nico and 0.1 mg/L DBA, 0.1 mg/L DBA alone, and an untreated control group. After 24 hours of cultivation, root tissues were collected for the assessment of physiological indices, transcriptomic profiling, and metabolomic analysis.
"],"omics_type":["Metabolomics"],"study_design":["Metabolomics","targeted analysis","AB SCIEX TripleTOF 5600-","Pesticide stress","Shimadzu Nexera UHPLC system","Brassica rapa var. perviridis","nicosulfuron","environmental adaptation","Pseudomonas","metabolic crosstalk","experimental sample","root tissues"],"curator_keywords":["Metabolomics","targeted analysis","AB SCIEX TripleTOF 5600-","Pesticide stress","Shimadzu Nexera UHPLC system","Brassica rapa var. perviridis","nicosulfuron","environmental adaptation","Pseudomonas","metabolic crosstalk","experimental sample","root tissues"],"mass_spectrometry_protocol":["Root samples (0.50 g) were homogenized in a methanol solution (80% v/v, 4 mL). Following a 15-minute vortexing, the mixture was centrifuged at 12,000 × g for 10 minutes. The supernatant was then filtered through a 0.22 μm filter into brown autosampler vials for metabolomic analysis.
Metabolic profile for each sample was detected using a Sciex TripleTOF 5600+ coupled with a Shimadzu LC-20A HPLC. Electrospray ionization (ESI) in both positive and negative modes was performed for mass spectrometry. The chromatographic column was a Waters XSelect HSS T3 column (4.6×150 mm, 3.5 µm) with the flow rate set at 0.30 mL/min. Mobile phase A was prepared using 0.1% formic acid solution for positive ionization mode and 5 mM ammonium formate solution for negative ionization mode. Mobile phase B consisted of acetonitrile and was programmed at 1% for 0−3.0 min, from 1% to 100% with a linear ramp for 3.1−24.0 min, 100% for 24.1−32.0 min, and 1% for 32.1−37.0 min.
"],"additional_accession":[]},"is_claimable":false,"name":"Plants establish metabolic crosstalk with Pseudomonas for enhancing herbicide-stress resistance","description":"Although it is known that plants can recruit beneficial rhizobacteria under various stresses, the mechanisms underlying their synergistic interaction in regulating plant resistance remain poorly understood. This study demonstrates that plants establish metabolic crosstalk with Pseudomonas for enhancing herbicide-stress resistance. Exposure to nicosulfuron (Nico) triggered the significant enrichment of Pseudomonas in both the rhizosphere and endosphere of Brassica rapa var. perviridis. Notably, several Pseudomonas isolates, particularly strain RL11, effectively alleviated Nico-induced stress in B. rapa despite lacking direct degradation capabilities. This beneficial interaction involves two phases of metabolic crosstalk between B. rapa and strain RL11. In the rhizosphere, B. rapa in response to Nico stress promoted the secretion of choline and uracil in root exudates, facilitating the recruitment and colonization of strain RL11. Following colonization, strain RL11 exchanged metabolites with the host plants and released several bioactive compounds in the endosphere, particularly 2,3-dihydroxybenzoic acid (DBA), tyramine, and pantothenic acid, which helped alleviate Nico-induced stress. Notably, DBA activated B. rapa detoxification and upregulated the biosynthesis of defense metabolites (polyphenols and glucosinolates). Furthermore, DBA enhanced the resistance of both B. rapa and rice to various herbicides (isoproturon and acetochlor). Our findings provide novel insights into the synergistic interaction between stressed plants and microbes and offer new strategies for developing microbe-derived biostimulants to enhance plant stress adaptability.","dates":{"publication":"2026-09-12","submission":"2026-09-11"},"accession":"MTBLS15629","cross_references":{}}